An allometric smoothing function to describe the relation between otolith and somatic growth over the lifespan of walleye pollock (Theragra chalcogramma)

We propose a new equation to describe the relation between otolith length (OL) and somatic length (fork length [FL]) of fish for the entire lifespan of the fish. The equation was developed by applying a mathematical smoothing method based on an allometric equation with a constant term for walleye pollock (Theragra chalcogramma) —a species that shows an extended longevity (>20 years). The most appropriate equation for defining the relation between OL and FL was a four-phase allometric smoothing function with three inflection points. The inflection points correspond to the timing of settlement of walleye pollock, changes in sexual maturity, and direction of otolith growth. Allometric smoothing functions describing the relation between short otolith radius and FL, long otolith radius and FL, and FL and body weight were also developed. The proposed allometric smoothing functions cover the entire lifespan of walleye pollock. We term these equations “allometric smoothing functions for otolith and somatic growth over the lifespan of walleye pollock.”

A novel brain partition highlights the modular skeleton shared by structure and function

Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent progress in neuroimaging has helped advance our understanding of this important issue, with diffusion images providing information about structural connectivity (SC) and functional magnetic resonance imaging shedding light on resting state functional connectivity (rsFC). Here, we adopt a systems approach, relying on modular hierarchical clustering, to study together SC and rsFC datasets gathered independently from healthy human subjects. Our novel approach allows us to find a common skeleton shared by structure and function from which a new, optimal, brain partition can be extracted. We describe the emerging common structure-function modules (SFMs) in detail and compare them with commonly employed anatomical or functional parcellations. Our results underline the strong correspondence between brain structure and resting-state dynamics as well as the emerging coherent organization of the human brain.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

Ecosystem function and biodiversity on coral reefs

The article highlights a workshop held in Key West, Florida in November 1993 attended by a group of 35 international scientists where topics of ecosystem function and biodiversity on coral reefs were discussed.

Análise matemática de soluções descontínuas de leis de conservação hiperbólicas e resoluções numéricas para a captura de ondas de choque em escoamentos multifásicos em meios porosos

O processo de recuperação secundária de petróleo é comumente realizado com a injeção de água ou gás no reservatório a fim de manter a pressão necessária para sua extração. Para que o investimento seja viável, os gastos com a extração precisam ser menores do que o retorno financeiro obtido com a produção de petróleo. Objetivando-se estudar possíveis cenários para o processo de exploração, costuma-se utilizar simulações dos processos de extração. As equações que modelam esse processo de recuperação são de caráter hiperbólico e não lineares, as quais podem ser interpretadas como Leis de Conservação, cujas soluções são complexas por suas naturezas descontínuas. Essas descontinuidades ou saltos são conhecidas como ondas de choque. Neste trabalho foi abordada uma análise matemática para os fenômenos oriundos de leis de conservação, para em seguida utilizá-la no entendimento do referido problema. Foram estudadas soluções fracas que, fisicamente, podem ser interpretadas como ondas de choque ou rarefação, então, para que fossem distinguidas as fisicamente admissíveis, foi considerado o princípio de entropia, nas suas diversas formas. As simulações foram realizadas nos âmbitos dos escoamentos bifásicos e trifásicos, em que os fluidos são imiscíveis e os efeitos gravitacionais e difusivos, devido à pressão capilar, foram desprezados. Inicialmente, foi feito um estudo comparativo de resoluções numéricas na captura de ondas de choque em escoamento bifásico água-óleo. Neste estudo destacam-se o método Composto LWLF-k, o esquema NonStandard e a introdução da nova função de renormalização para o esquema NonStandard, onde obteve resultados satisfatórios, principalmente em regiões onde a viscosidade do óleo é muito maior do que a viscosidade da água. No escoamento bidimensional, um novo método é proposto, partindo de uma generalização do esquema NonStandard unidimensional. Por fim, é feita uma adaptação dos métodos LWLF-4 e NonStandard para a simulação em escoamentos trifásicos em domínios unidimensional. O esquema NonStandard foi considerado mais eficiente nos problemas abordados, uma vez que sua versão bidimensional mostrou-se satisfatória na captura de ondas de choque em escoamentos bifásicos em meios porosos.